The Mediterranean Sea is a hotspot of biodiversity, originating as the result of various geological, climatic and hydrological transformations, including alternating glacial and interglacial periods during the Quaternary. There is a long tradition of descriptive studies in the Mediterranean Sea, whereas manipulative experiments have been introduced in the 1990s with an initial focus on biological interactions. Experiments are now increasingly used to examining species interactions in relation to regional stressors and global threats such as ocean warming, acidification, extreme climate events and biological invasions. We offer a synthesis of this research using regime shifts as a unifying concept. We start with a brief introduction to regime shifts and the underlying theory, followed by a discussion of ongoing regime shifts in the Mediterranean, such as the transition from macroalgal forests to turf-dominated assemblages and the collapse of sessile organisms in response to heatwaves, species invasions, infectious diseases and pest metabolites. We then examine the implications of threshold-like biological responses and hysteresis for habitat restoration and rehabilitation. We conclude with an overview of the research that is needed to understand the interplay between species interactions and rapid environmental change, for which the Mediterranean is providing several dramatic examples.